4-145900258-C-A

Position:

• chr4-145900258-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306215.2(ZNF827):​c.1093+1908G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,222 control chromosomes in the GnomAD database, including 2,565 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2565 hom., cov: 32)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

Genes affected

ZNF827 (HGNC:27193): (zinc finger protein 827) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF827	NM_001306215.2	c.1093+1908G>T		intron_variant		ENST00000508784.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF827	ENST00000508784.6	c.1093+1908G>T		intron_variant		1	NM_001306215.2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23324 AN: 152104 Hom.: 2558 Cov.: 32

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.162

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23339 AN: 152222 Hom.: 2565 Cov.: 32 AF XY: 0.160 AC XY: 11905 AN XY: 74432

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.166

Alfa AF: 0.172 Hom.: 3381

Bravo AF: 0.157

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	9.8
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4835265; hg19: chr4-146821410;